[gmx-users] KALP in DPPC tutorial reg

[Justin Lemkul]

On 10/14/13 7:47 AM, Sathya wrote:
> Hi,
>
> I'm doing the KALP-15 IN DPPC through the Justin's tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
>   I have few questions. Please help me to solve it.
>
> 1) After the topol.top file has generated from pdb2gmx is it necessary to
> add DPPC 128 in the molecule section?.
>

If there are lipids in the coordinate file, there have to be lipids in the 
topology.  The tutorial walks you through all of this, step by step.

> 2) I have used DPPC 128 in the molecule section and during adding ions with
> the following command shows error.
> grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
> The above command shows this error.
>
> Fatal error:
> number of coordinates in coordinate file (system_solv.gro, 27162) does not
> match topology (topol.top, 33451)
>
> Please tell me where should i change to solve this problem.
>

If you're adding ions, that means you should have already done the insertion, 
inflation/packing, and solvation steps.  You will not have 128 lipids at that 
point (as is stated in the tutorial).  You have a significant mismatch 
somewhere, though, and the difference is nowhere close to being only a problem 
with the lipids.

> 3) If i didnt use DPPC in molecule section of .top file while running
> equilibration using make_ndx which ask us to enter the protein+lipids i
> could not find the DPPC option there..
>

You don't make index groups from the topology; you make them from coordinate 
files.  If DPPC wasn't an option when running make_ndx, then you didn't have 
lipids present.  I believe this questions was just asked the other day.

Given the magnitude of problems you're experiencing, I would suggest starting 
the tutorial over and checking your output at every step more carefully.  There 
seem to be some fundamental problems in whatever you have done.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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